DNA Microarray-Based Mutation Discovery and Genotyping

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

DNA microarrays provide an efficient means of identifying single-nucleotide polymorphisms (SNPs) in DNA samples and characterizing their frequencies in individual and mixed samples. We have studied the parameters that determine the sensitivity of DNA probes to SNPs and found that the melting temperature (Tm) of the probe is the primary determinant of probe sensitivity. An isothermal-melting temperature DNA microarray design, in which the Tm of all probes is tightly distributed, can be implemented by varying the length of DNA probes within a single DNA microarray. I describe guidelines for designing isothermal-melting temperature DNA microarrays and protocols for labeling and hybridizing DNA samples to DNA microarrays for SNP discovery, genotyping, and quantitative determination of allele frequencies in mixed samples.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages179-191
Number of pages13
DOIs
StatePublished - 2011

Publication series

NameMethods in Molecular Biology
Volume772
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • Bulk segregant mapping
  • DNA microarray
  • Isothermal melting temperature
  • Single-nucleotide polymorphisms
  • SNPscanner

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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